Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

doi:10.1186/1748-7188-2-13

Algorithms for Molecular Biology

Volume 2

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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Valentina Boeva¹^,2 , Julien Clément³ , Mireille Régnier² , Mikhail A Roytberg⁴^,5 and Vsevolod J Makeev¹^,6

¹Institute of Genetics and Selection of Industrial Microorganisms, GosNIIGenetika, 117545 Moscow, Russia

²MIGEC, INRIA Rocquencourt, 78153 Le Chesnay, France

³GREYC, CNRS UMR 6072, Laboratoire d'informatique, 14032 Caen, France

⁴Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Puschino, Moscow Region, Russia

⁵Puschino State University, Puschino, Moscow Region, Russia

⁶Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

author email corresponding author email

Algorithms for Molecular Biology 2007, 2:13doi:10.1186/1748-7188-2-13


Published:	10 October 2007

Additional files

Additional file 1:

Bernoulli text model. Probability to find multiple occurrences of a single motif. The detailed description of the algorithm for the p-value calculation in the case of multiple occurrences of a single motif.

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Additional file 2:

Tree construction from PWM motif representation. The brief description of the procedure of the prefix tree construction from PWM motif representation.

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Additional file 3:

Tree construction from PWM motif representation. Steps of the prefix tree construction for a PWM and a given cut-off.

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